Neglected tropical diseases (NTDs) cause significant physical debilitation, lowered economic productivity, and social ostracism for afflicted individuals. Five NTDs with available preventive chemotherapy: lymphatic filariasis (LF), trachoma, schistosomiasis, onchocerciasis and the three soil-transmitted helminths (STH); have been targeted for control or elimination, but resource constraints in endemic countries have impeded progress toward these goals. We have developed an integrated mapping protocol, Integrated Threshold Mapping (ITM) for use by Ministries of Health to decide where public health interventions for NTDs are needed.